X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=01353d893f56dfd4803356249fd9db4fff83586d;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=90b9f6a786ec1526a5f8faf1ec3ba1dc108efaac;hpb=7ba92fd0e87b8155e656cfb9562d024a2524086d;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 90b9f6a..01353d8 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -28,10 +28,13 @@ import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignExportSettingI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; @@ -50,6 +53,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; @@ -237,6 +241,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this(al, hiddenColumns, width, height, null); } + /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId @@ -286,6 +291,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, init(); } + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection hiddenColumns, int width, int height) + { + setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + alignPanel = new AlignmentPanel(this, viewport); + addAlignmentPanel(alignPanel, true); + init(); + } + + /** * Make a new AlignFrame from existing alignmentPanels * @@ -1095,11 +1122,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - /* - * First save any linked Chimera session. - */ - Desktop.instance.saveChimeraSessions(file); - success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( @@ -1118,32 +1140,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return false; } - String[] omitHidden = null; - - if (viewport.hasHiddenColumns()) - { - int reply = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager - .getString("label.alignment_contains_hidden_columns"), - MessageManager - .getString("action.save_omit_hidden_columns"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); - - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } - } - FeatureRenderer fr = new FeatureRenderer(this.alignPanel); - viewport.setFeatureRenderer(fr); - FormatAdapter f = new FormatAdapter(viewport); + ExportData exportData = getAlignmentForExport(format); + FormatAdapter f = new FormatAdapter(alignPanel); String output = f.formatSequences(format, - viewport.getAlignment(), // class cast exceptions will + exportData.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), viewport.getColumnSelection()); if (output == null) @@ -1184,6 +1187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } + private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) @@ -1208,35 +1212,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - String[] omitHidden = null; - FeatureRenderer fr = new FeatureRenderer(this.alignPanel); - viewport.setFeatureRenderer(fr); - if (viewport.hasHiddenColumns()) - { - int reply = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager - .getString("label.alignment_contains_hidden_columns"), - MessageManager - .getString("action.save_omit_hidden_columns"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } + ExportData exportData = getAlignmentForExport(e.getActionCommand()); + if (exportData.getSettings().isCancelled()) + { + return; } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - try { - cap.setText(new FormatAdapter(viewport).formatSequences( + cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) + .formatSequences( e.getActionCommand(), - viewport.getAlignment(), omitHidden, + exportData.getAlignment(), + exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getColumnSelection())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new Object[] @@ -1249,6 +1239,105 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } + public ExportData getAlignmentForExport(String exportFomat) + { + AlignmentI alignmentToExport = null; + String[] omitHidden = null; + int[] alignmentStartEnd = new int[2]; + + HiddenSequences hiddenSeqs = viewport.getAlignment() + .getHiddenSequences(); + + + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = new int[] + { 0, alignmentToExport.getWidth() - 1 }; + + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFomat); + settings.isExportAnnotations(); + + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false); + } + + if (hasHiddenSeqs && settings.isExportHiddenSequences()) + { + alignmentToExport = hiddenSeqs.getFullAlignment(); + } + else + { + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport + .getColumnSelection().getHiddenColumns()); + } + return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd, + settings); + } + + private static int[] getStartEnd(int[] aligmentStartEnd, + List hiddenCols) + { + int startPos = aligmentStartEnd[0]; + int endPos = aligmentStartEnd[1]; + + int[] lowestRange = new int[2]; + int[] higestRange = new int[2]; + + for (int[] hiddenCol : hiddenCols) + { + // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]); + + lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; + higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; + } + // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]); + // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]); + + if (lowestRange[0] == 0 && lowestRange[1] == 0) + { + startPos = aligmentStartEnd[0]; + } + else + { + startPos = lowestRange[1] + 1; + } + + if (higestRange[0] == 0 && higestRange[1] == 0) + { + endPos = aligmentStartEnd[1]; + } + else + { + endPos = higestRange[0]; + } + + // System.out.println("Export range : " + minPos + " - " + maxPos); + return new int[] + { startPos, endPos }; + } + + public static void main(String[] args) + { + ArrayList hiddenCols = new ArrayList(); + hiddenCols.add(new int[] + { 0, 4 }); + hiddenCols.add(new int[] + { 6, 9 }); + hiddenCols.add(new int[] + { 11, 12 }); + hiddenCols.add(new int[] + { 33, 33 }); + hiddenCols.add(new int[] + { 45, 50 }); + + int[] x = getStartEnd(new int[] + { 0, 50 }, hiddenCols); + // System.out.println("Export range : " + x[0] + " - " + x[1]); + } + /** * DOCUMENT ME! * @@ -1258,17 +1347,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - // new HTMLOutput(alignPanel, - // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(), - // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); new HtmlSvgOutput(null, alignPanel); } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, - alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } public void createImageMap(File file, String image) @@ -1773,7 +1858,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + omitHidden, null); StringSelection ss = new StringSelection(output); @@ -5985,6 +6070,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sf.setComplementVisible(this, show); } } + + public class ExportData + { + private AlignmentI alignment; + + private String[] omitHidden; + + private int[] startEnd; + + private AlignExportSettingI settings; + + public ExportData(AlignmentI align, String[] ommit, int[] startEnd, + AlignExportSettingI settings) + { + this.alignment = align; + this.omitHidden = ommit; + this.startEnd = startEnd; + this.settings = settings; + } + + public AlignmentI getAlignment() + { + return alignment; + } + + public void setAlignment(AlignmentI alignment) + { + this.alignment = alignment; + } + + public String[] getOmitHidden() + { + return omitHidden; + } + + public void setOmitHidden(String[] omitHidden) + { + this.omitHidden = omitHidden; + } + + public int[] getStartEndPostions() + { + return startEnd; + } + + public void setStartEndPostions(int[] startEnd) + { + this.startEnd = startEnd; + } + + public AlignExportSettingI getSettings() + { + return settings; + } + + public void setSettings(AlignExportSettingI settings) + { + this.settings = settings; + } + } + } class PrintThread extends Thread